data_4MS9 # _entry.id 4MS9 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 4MS9 pdb_00004ms9 10.2210/pdb4ms9/pdb NDB NA2738 ? ? RCSB RCSB082302 ? ? WWPDB D_1000082302 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2014-02-12 2 'Structure model' 1 1 2014-03-19 3 'Structure model' 1 2 2018-01-24 4 'Structure model' 1 3 2020-02-26 5 'Structure model' 1 4 2024-02-28 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Structure summary' 3 4 'Structure model' 'Data collection' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' audit_author 2 4 'Structure model' reflns 3 5 'Structure model' chem_comp_atom 4 5 'Structure model' chem_comp_bond 5 5 'Structure model' database_2 6 5 'Structure model' pdbx_struct_conn_angle 7 5 'Structure model' struct_conn 8 5 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_audit_author.name' 2 4 'Structure model' '_reflns.pdbx_Rmerge_I_obs' 3 5 'Structure model' '_database_2.pdbx_DOI' 4 5 'Structure model' '_database_2.pdbx_database_accession' 5 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 6 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 7 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 8 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 9 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 10 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 11 5 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 12 5 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 13 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 14 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 15 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 16 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 17 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 18 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 19 5 'Structure model' '_pdbx_struct_conn_angle.value' 20 5 'Structure model' '_struct_conn.pdbx_dist_value' 21 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 22 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 23 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 24 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 25 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 26 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 27 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 28 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 29 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 30 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 31 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 32 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 33 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 34 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4MS9 _pdbx_database_status.recvd_initial_deposition_date 2013-09-18 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4MSB . unspecified PDB 4MSR . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Sheng, J.' 1 'Li, L.' 2 'Engelhart, A.E.' 3 'Gan, J.' 4 'Wang, J.' 5 'Szostak, J.W.' 6 # _citation.id primary _citation.title ;Structural insights into the effects of 2'-5' linkages on the RNA duplex. ; _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 111 _citation.page_first 3050 _citation.page_last 3055 _citation.year 2014 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24516151 _citation.pdbx_database_id_DOI 10.1073/pnas.1317799111 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Sheng, J.' 1 ? primary 'Li, L.' 2 ? primary 'Engelhart, A.E.' 3 ? primary 'Gan, J.' 4 ? primary 'Wang, J.' 5 ? primary 'Szostak, J.W.' 6 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'Native RNA duplex 10mer' 3206.980 1 ? ? ? ? 2 non-polymer syn 'STRONTIUM ION' 87.620 3 ? ? ? ? 3 water nat water 18.015 57 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code CCGGCGCCGG _entity_poly.pdbx_seq_one_letter_code_can CCGGCGCCGG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'STRONTIUM ION' SR 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 C n 1 3 G n 1 4 G n 1 5 C n 1 6 G n 1 7 C n 1 8 C n 1 9 G n 1 10 G n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'Solid Phase Synthesis and HPLC purification' # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 SR non-polymer . 'STRONTIUM ION' ? 'Sr 2' 87.620 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 C 1 1 1 C C A . n A 1 2 C 2 2 2 C C A . n A 1 3 G 3 3 3 G G A . n A 1 4 G 4 4 4 G G A . n A 1 5 C 5 5 5 C C A . n A 1 6 G 6 6 6 G G A . n A 1 7 C 7 7 7 C C A . n A 1 8 C 8 8 8 C C A . n A 1 9 G 9 9 9 G G A . n A 1 10 G 10 10 10 G G A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 SR 1 101 1 SR SR A . C 2 SR 1 102 2 SR SR A . D 2 SR 1 103 3 SR SR A . E 3 HOH 1 201 3 HOH HOH A . E 3 HOH 2 202 4 HOH HOH A . E 3 HOH 3 203 5 HOH HOH A . E 3 HOH 4 204 6 HOH HOH A . E 3 HOH 5 205 7 HOH HOH A . E 3 HOH 6 206 8 HOH HOH A . E 3 HOH 7 207 9 HOH HOH A . E 3 HOH 8 208 10 HOH HOH A . E 3 HOH 9 209 11 HOH HOH A . E 3 HOH 10 210 12 HOH HOH A . E 3 HOH 11 211 13 HOH HOH A . E 3 HOH 12 212 14 HOH HOH A . E 3 HOH 13 213 15 HOH HOH A . E 3 HOH 14 214 16 HOH HOH A . E 3 HOH 15 215 17 HOH HOH A . E 3 HOH 16 216 18 HOH HOH A . E 3 HOH 17 217 19 HOH HOH A . E 3 HOH 18 218 20 HOH HOH A . E 3 HOH 19 219 21 HOH HOH A . E 3 HOH 20 220 22 HOH HOH A . E 3 HOH 21 221 23 HOH HOH A . E 3 HOH 22 222 24 HOH HOH A . E 3 HOH 23 223 25 HOH HOH A . E 3 HOH 24 224 26 HOH HOH A . E 3 HOH 25 225 27 HOH HOH A . E 3 HOH 26 226 28 HOH HOH A . E 3 HOH 27 227 30 HOH HOH A . E 3 HOH 28 228 31 HOH HOH A . E 3 HOH 29 229 32 HOH HOH A . E 3 HOH 30 230 33 HOH HOH A . E 3 HOH 31 231 34 HOH HOH A . E 3 HOH 32 232 35 HOH HOH A . E 3 HOH 33 233 36 HOH HOH A . E 3 HOH 34 234 37 HOH HOH A . E 3 HOH 35 235 38 HOH HOH A . E 3 HOH 36 236 39 HOH HOH A . E 3 HOH 37 237 40 HOH HOH A . E 3 HOH 38 238 41 HOH HOH A . E 3 HOH 39 239 42 HOH HOH A . E 3 HOH 40 240 43 HOH HOH A . E 3 HOH 41 241 45 HOH HOH A . E 3 HOH 42 242 48 HOH HOH A . E 3 HOH 43 243 49 HOH HOH A . E 3 HOH 44 244 50 HOH HOH A . E 3 HOH 45 245 53 HOH HOH A . E 3 HOH 46 246 54 HOH HOH A . E 3 HOH 47 247 55 HOH HOH A . E 3 HOH 48 248 56 HOH HOH A . E 3 HOH 49 249 58 HOH HOH A . E 3 HOH 50 250 59 HOH HOH A . E 3 HOH 51 251 60 HOH HOH A . E 3 HOH 52 252 63 HOH HOH A . E 3 HOH 53 253 71 HOH HOH A . E 3 HOH 54 254 74 HOH HOH A . E 3 HOH 55 255 75 HOH HOH A . E 3 HOH 56 256 76 HOH HOH A . E 3 HOH 57 257 78 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal HKL-2000 'data collection' . ? 1 ACORN phasing . ? 2 REFMAC refinement 5.6.0117 ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # _cell.entry_id 4MS9 _cell.length_a 22.708 _cell.length_b 22.708 _cell.length_c 77.721 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 4MS9 _symmetry.space_group_name_H-M 'P 31 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4MS9 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.80 _exptl_crystal.density_percent_sol 31.81 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details ;10% MPD (2-methyl-2,4-pentanediol), 40 mM sodium cacodylate pH 6.0, 12 mM spermine tetrahydrochloride, and 80 mM strontium (II) chloride , VAPOR DIFFUSION, HANGING DROP, temperature 293K ; _exptl_crystal_grow.pdbx_pH_range ? # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 100 ? 1 2 ? ? 1 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 CCD 'ADSC QUANTUM 315' 2013-01-10 ? 2 CCD 'ADSC QUANTUM 315r' ? ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Double Crystal Si (111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0 _diffrn_radiation_wavelength.wt 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_wavelength_list 1 SYNCHROTRON 'ALS BEAMLINE 8.2.2' ALS 8.2.2 ? 1.0 2 SYNCHROTRON 'ALS BEAMLINE 8.2.1' ALS 8.2.1 ? 1.0 # _reflns.entry_id 4MS9 _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 50 _reflns.d_resolution_high 1.32 _reflns.number_obs 5742 _reflns.number_all 5981 _reflns.percent_possible_obs 96 _reflns.pdbx_Rmerge_I_obs 0.055 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 33.1 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 11.8 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_CC_half ? _reflns.pdbx_CC_star ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_Rrim_I_all ? # _reflns_shell.d_res_high 1.32 _reflns_shell.d_res_low 1.37 _reflns_shell.percent_possible_all 84.7 _reflns_shell.Rmerge_I_obs 0.225 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 8.28 _reflns_shell.pdbx_redundancy 10.4 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 480 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_Rrim_I_all ? # _refine.entry_id 4MS9 _refine.ls_number_reflns_obs 5463 _refine.ls_number_reflns_all 5626 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F -3 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 25.91 _refine.ls_d_res_high 1.32 _refine.ls_percent_reflns_obs 97.08 _refine.ls_R_factor_obs 0.19016 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.18843 _refine.ls_R_factor_R_free 0.22753 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.5 _refine.ls_number_reflns_R_free 256 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.961 _refine.correlation_coeff_Fo_to_Fc_free 0.949 _refine.B_iso_mean 16.061 _refine.aniso_B[1][1] -0.03 _refine.aniso_B[2][2] -0.03 _refine.aniso_B[3][3] 0.05 _refine.aniso_B[1][2] -0.02 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'AB INITIO PHASING' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.064 _refine.pdbx_overall_ESU_R_Free 0.069 _refine.overall_SU_ML 0.042 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 1.022 _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 4MS9 _refine_analyze.Luzzati_coordinate_error_obs 0.064 _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free 0.069 _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 212 _refine_hist.pdbx_number_atoms_ligand 3 _refine_hist.number_atoms_solvent 57 _refine_hist.number_atoms_total 272 _refine_hist.d_res_high 1.32 _refine_hist.d_res_low 25.91 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 0.015 0.011 ? 236 ? 'X-RAY DIFFRACTION' r_bond_other_d ? ? ? ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1.706 1.430 ? 367 ? 'X-RAY DIFFRACTION' r_angle_other_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_chiral_restr 0.082 0.200 ? 40 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.028 0.020 ? 105 ? 'X-RAY DIFFRACTION' r_gen_planes_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbd_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbd_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbtor_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbtor_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_xyhbond_nbd_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_xyhbond_nbd_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_metal_ion_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_metal_ion_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_vdw_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_vdw_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_hbond_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_hbond_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_metal_ion_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_metal_ion_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcbond_it ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcbond_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcangle_it ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcangle_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_scbond_it ? ? ? ? ? 'X-RAY DIFFRACTION' r_scbond_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_scangle_it ? ? ? ? ? 'X-RAY DIFFRACTION' r_scangle_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_long_range_B_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_long_range_B_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_rigid_bond_restr ? ? ? ? ? 'X-RAY DIFFRACTION' r_sphericity_free ? ? ? ? ? 'X-RAY DIFFRACTION' r_sphericity_bonded ? ? ? ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.323 _refine_ls_shell.d_res_low 1.357 _refine_ls_shell.number_reflns_R_work 313 _refine_ls_shell.R_factor_R_work 0.231 _refine_ls_shell.percent_reflns_obs 90.53 _refine_ls_shell.R_factor_R_free 0.219 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 12 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.R_factor_obs ? # _database_PDB_matrix.entry_id 4MS9 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 4MS9 _struct.title 'Native RNA-10mer Structure: ccggcgccgg' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4MS9 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA native duplex 10mer, RNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 2 ? D N N 2 ? E N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4MS9 _struct_ref.pdbx_db_accession 4MS9 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code CCGGCGCCGG _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4MS9 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 10 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 4MS9 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 10 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 10 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2230 ? 1 MORE -171 ? 1 'SSA (A^2)' 3850 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 4_555 y,x,-z -0.5000000000 0.8660254038 0.0000000000 0.0000000000 0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? A G 4 O6 ? ? ? 1_555 B SR . SR ? ? A G 4 A SR 101 1_555 ? ? ? ? ? ? ? 2.739 ? ? metalc2 metalc ? ? A G 10 "O3'" ? ? ? 1_555 C SR . SR ? ? A G 10 A SR 102 1_555 ? ? ? ? ? ? ? 2.566 ? ? metalc3 metalc ? ? A G 10 "O2'" ? ? ? 1_555 D SR . SR ? ? A G 10 A SR 103 1_555 ? ? ? ? ? ? ? 2.526 ? ? metalc4 metalc ? ? A G 10 "O3'" ? ? ? 1_555 D SR . SR ? ? A G 10 A SR 103 1_555 ? ? ? ? ? ? ? 2.683 ? ? metalc5 metalc ? ? B SR . SR ? ? ? 1_555 E HOH . O ? ? A SR 101 A HOH 202 1_555 ? ? ? ? ? ? ? 2.661 ? ? metalc6 metalc ? ? B SR . SR ? ? ? 1_555 E HOH . O ? ? A SR 101 A HOH 206 1_555 ? ? ? ? ? ? ? 2.537 ? ? metalc7 metalc ? ? B SR . SR ? ? ? 1_555 E HOH . O ? ? A SR 101 A HOH 227 1_555 ? ? ? ? ? ? ? 2.580 ? ? metalc8 metalc ? ? B SR . SR ? ? ? 1_555 E HOH . O ? ? A SR 101 A HOH 246 1_555 ? ? ? ? ? ? ? 2.360 ? ? metalc9 metalc ? ? B SR . SR ? ? ? 1_555 E HOH . O ? ? A SR 101 A HOH 247 1_555 ? ? ? ? ? ? ? 2.491 ? ? metalc10 metalc ? ? C SR . SR ? ? ? 1_555 E HOH . O ? ? A SR 102 A HOH 249 1_555 ? ? ? ? ? ? ? 2.834 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 A G 10 N1 ? ? A C 1 A G 10 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 A G 10 O6 ? ? A C 1 A G 10 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 A G 10 N2 ? ? A C 1 A G 10 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 A G 9 N1 ? ? A C 2 A G 9 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 A G 9 O6 ? ? A C 2 A G 9 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 A G 9 N2 ? ? A C 2 A G 9 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 8 N3 ? ? A G 3 A C 8 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 A C 8 O2 ? ? A G 3 A C 8 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 A C 8 N4 ? ? A G 3 A C 8 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 7 N3 ? ? A G 4 A C 7 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 7 O2 ? ? A G 4 A C 7 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 7 N4 ? ? A G 4 A C 7 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 6 N1 ? ? A C 5 A G 6 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 6 O6 ? ? A C 5 A G 6 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 6 N2 ? ? A C 5 A G 6 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 6 N1 ? ? ? 1_555 A C 5 N3 ? ? A G 6 A C 5 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 6 N2 ? ? ? 1_555 A C 5 O2 ? ? A G 6 A C 5 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 6 O6 ? ? ? 1_555 A C 5 N4 ? ? A G 6 A C 5 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 7 N3 ? ? ? 1_555 A G 4 N1 ? ? A C 7 A G 4 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 7 N4 ? ? ? 1_555 A G 4 O6 ? ? A C 7 A G 4 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 7 O2 ? ? ? 1_555 A G 4 N2 ? ? A C 7 A G 4 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 8 N3 ? ? ? 1_555 A G 3 N1 ? ? A C 8 A G 3 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 8 N4 ? ? ? 1_555 A G 3 O6 ? ? A C 8 A G 3 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 8 O2 ? ? ? 1_555 A G 3 N2 ? ? A C 8 A G 3 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 9 N1 ? ? ? 1_555 A C 2 N3 ? ? A G 9 A C 2 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 9 N2 ? ? ? 1_555 A C 2 O2 ? ? A G 9 A C 2 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 9 O6 ? ? ? 1_555 A C 2 N4 ? ? A G 9 A C 2 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 1 N3 ? ? A G 10 A C 1 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 1 O2 ? ? A G 10 A C 1 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 1 N4 ? ? A G 10 A C 1 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O6 ? A G 4 ? A G 4 ? 1_555 SR ? B SR . ? A SR 101 ? 1_555 O ? E HOH . ? A HOH 202 ? 1_555 108.8 ? 2 O6 ? A G 4 ? A G 4 ? 1_555 SR ? B SR . ? A SR 101 ? 1_555 O ? E HOH . ? A HOH 206 ? 1_555 83.6 ? 3 O ? E HOH . ? A HOH 202 ? 1_555 SR ? B SR . ? A SR 101 ? 1_555 O ? E HOH . ? A HOH 206 ? 1_555 77.7 ? 4 O6 ? A G 4 ? A G 4 ? 1_555 SR ? B SR . ? A SR 101 ? 1_555 O ? E HOH . ? A HOH 227 ? 1_555 70.6 ? 5 O ? E HOH . ? A HOH 202 ? 1_555 SR ? B SR . ? A SR 101 ? 1_555 O ? E HOH . ? A HOH 227 ? 1_555 69.3 ? 6 O ? E HOH . ? A HOH 206 ? 1_555 SR ? B SR . ? A SR 101 ? 1_555 O ? E HOH . ? A HOH 227 ? 1_555 127.6 ? 7 O6 ? A G 4 ? A G 4 ? 1_555 SR ? B SR . ? A SR 101 ? 1_555 O ? E HOH . ? A HOH 246 ? 1_555 133.7 ? 8 O ? E HOH . ? A HOH 202 ? 1_555 SR ? B SR . ? A SR 101 ? 1_555 O ? E HOH . ? A HOH 246 ? 1_555 81.3 ? 9 O ? E HOH . ? A HOH 206 ? 1_555 SR ? B SR . ? A SR 101 ? 1_555 O ? E HOH . ? A HOH 246 ? 1_555 141.7 ? 10 O ? E HOH . ? A HOH 227 ? 1_555 SR ? B SR . ? A SR 101 ? 1_555 O ? E HOH . ? A HOH 246 ? 1_555 71.6 ? 11 O6 ? A G 4 ? A G 4 ? 1_555 SR ? B SR . ? A SR 101 ? 1_555 O ? E HOH . ? A HOH 247 ? 1_555 120.6 ? 12 O ? E HOH . ? A HOH 202 ? 1_555 SR ? B SR . ? A SR 101 ? 1_555 O ? E HOH . ? A HOH 247 ? 1_555 117.4 ? 13 O ? E HOH . ? A HOH 206 ? 1_555 SR ? B SR . ? A SR 101 ? 1_555 O ? E HOH . ? A HOH 247 ? 1_555 72.5 ? 14 O ? E HOH . ? A HOH 227 ? 1_555 SR ? B SR . ? A SR 101 ? 1_555 O ? E HOH . ? A HOH 247 ? 1_555 159.5 ? 15 O ? E HOH . ? A HOH 246 ? 1_555 SR ? B SR . ? A SR 101 ? 1_555 O ? E HOH . ? A HOH 247 ? 1_555 89.8 ? 16 "O3'" ? A G 10 ? A G 10 ? 1_555 SR ? C SR . ? A SR 102 ? 1_555 O ? E HOH . ? A HOH 249 ? 1_555 83.4 ? 17 "O2'" ? A G 10 ? A G 10 ? 1_555 SR ? D SR . ? A SR 103 ? 1_555 "O3'" ? A G 10 ? A G 10 ? 1_555 62.2 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A SR 101 ? 7 'BINDING SITE FOR RESIDUE SR A 101' AC2 Software A SR 102 ? 4 'BINDING SITE FOR RESIDUE SR A 102' AC3 Software A SR 103 ? 3 'BINDING SITE FOR RESIDUE SR A 103' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 7 G A 4 ? G A 4 . ? 1_555 ? 2 AC1 7 HOH E . ? HOH A 202 . ? 1_555 ? 3 AC1 7 HOH E . ? HOH A 206 . ? 1_555 ? 4 AC1 7 HOH E . ? HOH A 220 . ? 4_555 ? 5 AC1 7 HOH E . ? HOH A 227 . ? 1_555 ? 6 AC1 7 HOH E . ? HOH A 246 . ? 1_555 ? 7 AC1 7 HOH E . ? HOH A 247 . ? 1_555 ? 8 AC2 4 G A 10 ? G A 10 . ? 1_555 ? 9 AC2 4 SR D . ? SR A 103 . ? 1_555 ? 10 AC2 4 HOH E . ? HOH A 210 . ? 1_555 ? 11 AC2 4 HOH E . ? HOH A 249 . ? 1_555 ? 12 AC3 3 G A 10 ? G A 10 . ? 1_555 ? 13 AC3 3 SR C . ? SR A 102 . ? 1_555 ? 14 AC3 3 HOH E . ? HOH A 232 . ? 5_434 ? # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 P _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 G _pdbx_validate_rmsd_bond.auth_seq_id_1 9 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 OP2 _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 G _pdbx_validate_rmsd_bond.auth_seq_id_2 9 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.382 _pdbx_validate_rmsd_bond.bond_target_value 1.485 _pdbx_validate_rmsd_bond.bond_deviation -0.103 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.017 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal C OP3 O N N 1 C P P N N 2 C OP1 O N N 3 C OP2 O N N 4 C "O5'" O N N 5 C "C5'" C N N 6 C "C4'" C N R 7 C "O4'" O N N 8 C "C3'" C N S 9 C "O3'" O N N 10 C "C2'" C N R 11 C "O2'" O N N 12 C "C1'" C N R 13 C N1 N N N 14 C C2 C N N 15 C O2 O N N 16 C N3 N N N 17 C C4 C N N 18 C N4 N N N 19 C C5 C N N 20 C C6 C N N 21 C HOP3 H N N 22 C HOP2 H N N 23 C "H5'" H N N 24 C "H5''" H N N 25 C "H4'" H N N 26 C "H3'" H N N 27 C "HO3'" H N N 28 C "H2'" H N N 29 C "HO2'" H N N 30 C "H1'" H N N 31 C H41 H N N 32 C H42 H N N 33 C H5 H N N 34 C H6 H N N 35 G OP3 O N N 36 G P P N N 37 G OP1 O N N 38 G OP2 O N N 39 G "O5'" O N N 40 G "C5'" C N N 41 G "C4'" C N R 42 G "O4'" O N N 43 G "C3'" C N S 44 G "O3'" O N N 45 G "C2'" C N R 46 G "O2'" O N N 47 G "C1'" C N R 48 G N9 N Y N 49 G C8 C Y N 50 G N7 N Y N 51 G C5 C Y N 52 G C6 C N N 53 G O6 O N N 54 G N1 N N N 55 G C2 C N N 56 G N2 N N N 57 G N3 N N N 58 G C4 C Y N 59 G HOP3 H N N 60 G HOP2 H N N 61 G "H5'" H N N 62 G "H5''" H N N 63 G "H4'" H N N 64 G "H3'" H N N 65 G "HO3'" H N N 66 G "H2'" H N N 67 G "HO2'" H N N 68 G "H1'" H N N 69 G H8 H N N 70 G H1 H N N 71 G H21 H N N 72 G H22 H N N 73 HOH O O N N 74 HOH H1 H N N 75 HOH H2 H N N 76 SR SR SR N N 77 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal C OP3 P sing N N 1 C OP3 HOP3 sing N N 2 C P OP1 doub N N 3 C P OP2 sing N N 4 C P "O5'" sing N N 5 C OP2 HOP2 sing N N 6 C "O5'" "C5'" sing N N 7 C "C5'" "C4'" sing N N 8 C "C5'" "H5'" sing N N 9 C "C5'" "H5''" sing N N 10 C "C4'" "O4'" sing N N 11 C "C4'" "C3'" sing N N 12 C "C4'" "H4'" sing N N 13 C "O4'" "C1'" sing N N 14 C "C3'" "O3'" sing N N 15 C "C3'" "C2'" sing N N 16 C "C3'" "H3'" sing N N 17 C "O3'" "HO3'" sing N N 18 C "C2'" "O2'" sing N N 19 C "C2'" "C1'" sing N N 20 C "C2'" "H2'" sing N N 21 C "O2'" "HO2'" sing N N 22 C "C1'" N1 sing N N 23 C "C1'" "H1'" sing N N 24 C N1 C2 sing N N 25 C N1 C6 sing N N 26 C C2 O2 doub N N 27 C C2 N3 sing N N 28 C N3 C4 doub N N 29 C C4 N4 sing N N 30 C C4 C5 sing N N 31 C N4 H41 sing N N 32 C N4 H42 sing N N 33 C C5 C6 doub N N 34 C C5 H5 sing N N 35 C C6 H6 sing N N 36 G OP3 P sing N N 37 G OP3 HOP3 sing N N 38 G P OP1 doub N N 39 G P OP2 sing N N 40 G P "O5'" sing N N 41 G OP2 HOP2 sing N N 42 G "O5'" "C5'" sing N N 43 G "C5'" "C4'" sing N N 44 G "C5'" "H5'" sing N N 45 G "C5'" "H5''" sing N N 46 G "C4'" "O4'" sing N N 47 G "C4'" "C3'" sing N N 48 G "C4'" "H4'" sing N N 49 G "O4'" "C1'" sing N N 50 G "C3'" "O3'" sing N N 51 G "C3'" "C2'" sing N N 52 G "C3'" "H3'" sing N N 53 G "O3'" "HO3'" sing N N 54 G "C2'" "O2'" sing N N 55 G "C2'" "C1'" sing N N 56 G "C2'" "H2'" sing N N 57 G "O2'" "HO2'" sing N N 58 G "C1'" N9 sing N N 59 G "C1'" "H1'" sing N N 60 G N9 C8 sing Y N 61 G N9 C4 sing Y N 62 G C8 N7 doub Y N 63 G C8 H8 sing N N 64 G N7 C5 sing Y N 65 G C5 C6 sing N N 66 G C5 C4 doub Y N 67 G C6 O6 doub N N 68 G C6 N1 sing N N 69 G N1 C2 sing N N 70 G N1 H1 sing N N 71 G C2 N2 sing N N 72 G C2 N3 doub N N 73 G N2 H21 sing N N 74 G N2 H22 sing N N 75 G N3 C4 sing N N 76 HOH O H1 sing N N 77 HOH O H2 sing N N 78 # _ndb_struct_conf_na.entry_id 4MS9 _ndb_struct_conf_na.feature 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A C 1 1_555 A G 10 4_555 0.072 -0.077 0.040 12.507 -13.201 -0.782 1 A_C1:G10_A A 1 ? A 10 ? 19 1 1 A C 2 1_555 A G 9 4_555 0.131 -0.144 -0.051 10.596 -17.332 0.782 2 A_C2:G9_A A 2 ? A 9 ? 19 1 1 A G 3 1_555 A C 8 4_555 -0.119 -0.169 0.065 0.757 -10.220 -1.653 3 A_G3:C8_A A 3 ? A 8 ? 19 1 1 A G 4 1_555 A C 7 4_555 -0.144 -0.037 0.092 -4.957 -17.116 3.616 4 A_G4:C7_A A 4 ? A 7 ? 19 1 1 A C 5 1_555 A G 6 4_555 0.186 -0.169 0.128 -1.102 -12.757 -1.844 5 A_C5:G6_A A 5 ? A 6 ? 19 1 1 A G 6 1_555 A C 5 4_555 -0.186 -0.169 0.128 1.102 -12.757 -1.843 6 A_G6:C5_A A 6 ? A 5 ? 19 1 1 A C 7 1_555 A G 4 4_555 0.144 -0.037 0.092 4.957 -17.116 3.616 7 A_C7:G4_A A 7 ? A 4 ? 19 1 1 A C 8 1_555 A G 3 4_555 0.119 -0.169 0.065 -0.757 -10.220 -1.653 8 A_C8:G3_A A 8 ? A 3 ? 19 1 1 A G 9 1_555 A C 2 4_555 -0.131 -0.144 -0.051 -10.596 -17.332 0.782 9 A_G9:C2_A A 9 ? A 2 ? 19 1 1 A G 10 1_555 A C 1 4_555 -0.072 -0.077 0.040 -12.507 -13.201 -0.782 10 A_G10:C1_A A 10 ? A 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A C 1 1_555 A G 10 4_555 A C 2 1_555 A G 9 4_555 -0.662 -1.978 3.297 -4.088 5.999 30.723 -4.715 0.485 2.930 11.129 7.584 31.549 1 AA_C1C2:G9G10_AA A 1 ? A 10 ? A 2 ? A 9 ? 1 A C 2 1_555 A G 9 4_555 A G 3 1_555 A C 8 4_555 -0.810 -1.738 3.398 -2.741 11.234 30.253 -5.026 0.989 2.661 20.603 5.028 32.339 2 AA_C2G3:C8G9_AA A 2 ? A 9 ? A 3 ? A 8 ? 1 A G 3 1_555 A C 8 4_555 A G 4 1_555 A C 7 4_555 0.718 -1.505 3.315 2.031 6.636 33.555 -3.576 -0.907 3.008 11.344 -3.471 34.245 3 AA_G3G4:C7C8_AA A 3 ? A 8 ? A 4 ? A 7 ? 1 A G 4 1_555 A C 7 4_555 A C 5 1_555 A G 6 4_555 -0.631 -1.212 3.129 -1.557 3.366 34.574 -2.514 0.832 3.026 5.644 2.610 34.766 4 AA_G4C5:G6C7_AA A 4 ? A 7 ? A 5 ? A 6 ? 1 A C 5 1_555 A G 6 4_555 A G 6 1_555 A C 5 4_555 0.000 -1.760 3.053 0.000 9.130 28.943 -4.936 0.000 2.399 17.719 0.000 30.319 5 AA_C5G6:C5G6_AA A 5 ? A 6 ? A 6 ? A 5 ? 1 A G 6 1_555 A C 5 4_555 A C 7 1_555 A G 4 4_555 0.631 -1.212 3.129 1.557 3.366 34.574 -2.514 -0.832 3.026 5.644 -2.610 34.766 6 AA_G6C7:G4C5_AA A 6 ? A 5 ? A 7 ? A 4 ? 1 A C 7 1_555 A G 4 4_555 A C 8 1_555 A G 3 4_555 -0.718 -1.505 3.315 -2.031 6.636 33.555 -3.576 0.907 3.008 11.344 3.471 34.245 7 AA_C7C8:G3G4_AA A 7 ? A 4 ? A 8 ? A 3 ? 1 A C 8 1_555 A G 3 4_555 A G 9 1_555 A C 2 4_555 0.810 -1.738 3.398 2.741 11.234 30.253 -5.026 -0.989 2.661 20.603 -5.028 32.339 8 AA_C8G9:C2G3_AA A 8 ? A 3 ? A 9 ? A 2 ? 1 A G 9 1_555 A C 2 4_555 A G 10 1_555 A C 1 4_555 0.662 -1.978 3.297 4.088 5.999 30.723 -4.715 -0.485 2.930 11.129 -7.584 31.549 9 AA_G9G10:C1C2_AA A 9 ? A 2 ? A 10 ? A 1 ? # _atom_sites.entry_id 4MS9 _atom_sites.fract_transf_matrix[1][1] 0.044037 _atom_sites.fract_transf_matrix[1][2] 0.025425 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.050850 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.012867 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P SR # loop_